Hi Lars, Here are a couple comments to supplement what Eric said. I believe you can draw an ellipsoid using VRML. You make a vrml Sphere node inside a Transform node. The Transform node scales the axes and rotates to get the desired ellipsoid.
How do I display a set of spheres, together with with some edges connecting them. I do like to show some kind of pseudo-molecule/graph.
The Tools/Volumes/Volume Path Tracer tool lets you place spheres (implemented as atoms), connected by cylinders (implemented as bonds) using the mouse. Or they can be read from an XML file. The Chimera user's guide, Tools section, Volume Path Tracer entry describes this. You can also call into the Path Tracer module to place them using your own Python code. The Phantom extension is an example of calling into the path tracer module to place spheres. Tom